Introduction

Biology is defined as the study of life / living things. A living thing is defined as anything that converts energy from one form to another, while using that energy to grow, change, and reproduce.

Scientific Method

The scientific method is the standard guideline for discovery and experimentation in the sciences (chemistry, physics, biology, etc..) The basic steps are...

1. Observe.
2. Ask a question about the observation.
3. Make a guess that answers the question (hypothesis).
4. Test the guess to see if it's correct (experiment).
5. Refine and iterate.

The last step (refine and iterate) just means that you do it all over again but make changes based on the things you learned from your experiment. For example, ...

• do additional experiments to dig into some aspect deeper.
• if the hypothesis wasn't supported by the experiment, maybe come up with a new hypothesis.

Hypothesis

The scientific method revolves around making an observation and coming up with a testable explanation for that observation -- called a hypothesis. If the explanation isn't testable, you can't consider it a hypothesis. For example, a good hypothesis may be that increased sun exposure leads to an increased risk of skin cancer because it's something you can test. A bad explanation may be that exposure to centaurs increase the risk of skin cancer because centaurs don't exist (and as such the hypothesis can't be tested).

Experiment

Once you have a hypothesis, you design an experiment to test it. In the case of our sun exposure leads to increased risk of skin cancer hypothesis, an experiment may be to expose skin cells to UV rays in amounts equivalent to that given off by the sun and then check to see if those cells have been damaged (compared to a control group of skin cells that you haven't exposed to UV rays).

What makes a good experiment?

• Control group - A control group contains a set of entities that don't get treatment, but those entities are equal to the entities in the experimental group (as much as possible) and exposed to the same conditions as the entities in the experimental group (as much as possible). This helps eliminate outside factors/variables from tainting the results of an experiment -- it's a controlled experiment . For example, in the skin cancer example experiment described above, a control group may be a set of skin cells that sit along side the experimental group skin cells that get treated with UV rays -- the cells in the control group shouldn't show signs of damage while the cells in the experimental group should.
• Random selection - The entities being used for an experiment must be randomly selected (both for the control group and the experimental group). Random selection helps minimize skewed results introduced from bias during the selection process. For example, the individual responsible for selecting candidates for drug trials may choose to disproportionately select people of a certain race (e.g. racism).
• Double blind - The people conducting the experiment may implicitly/explicitly taint the experiment via their own bias. For example, if the experiment involves an interviewer asking a set of questions, the interviewer may subconsciously change the pronunciations of words if he/she knows that the interviewee is in the control group, there by effecting the answer given by the interviewee.
• Statistical significance - The results between the control group and the experimental group needs to be large enough to support your hypothesis. A small difference could mean that outcome was due to variance in the selected groups (there's a branch of statistics that deals with this).
• Replicable - Others should be able to repeat the same experiment and (hopefully) come to the same result. If they don't, it could be that something was wrong with your experiment or the entities being tested had some underlying difference that changed the result.

Other terminology around the scientific method...

• treatment - The application of the test given to the experimental group(s) but not the control group.
• independent variable - An independent variable is basically the treatment you apply -- you can think of it as the input knob you control for your experiment. For example, in the skin cancer experiment, the independent variable would be the amount of artificial UV rays you apply to the skin cells.
• dependent variable - A dependent variable is a response you measure after applying the treatment -- you can think of it as the output from your experiment. For example, in the skin cancer experiment, the dependent variable might be a measurement of how different the cells are functioning (e.g. a cell with damaged DNA may produce different kinds / amounts of tRNA molecules -- something you can measure).
• data - This is exactly what you think it is -- measurements/observations made during the experiment.
• placebo effect - When experimenting on people, there's a phenomenon called the placebo effect: if someone takes something that shouldn't help them but are under the impression it will help them, it often times will help them, just from the psychological effect alone.

Chemistry

An element is matter that cannot be broken down any further by chemical reaction -- it's a substance made entirely out of one type of atom. Each element/atom has a specific set of properties that defines how it acts/reacts (e.g. weight, colour, how light reflects, etc..).

Examples of elements/atoms:

• Gold - Yellow coloured, reflective, malleable, and corrosion-resistant.
• Lead - Blue/white coloured, relatively soft, malleable.
• Carbon Silver/gray coloured, reflective, easily oxidizes/corrodes.

Examples of non-elements:

• Salt water - Mixture of sodium and water.
• Water - Water can be further broken down to the elements hydrogen and oxygen.
• Glucose - Glucose can be further broken down to the elements carbon, hydrogen, and oxygen.

The building blocks of atoms are protons, neutrons, and electrons. Protons and neutrons form the nucleus of the atom while electrons jump around outside of the nucleus. Protons and electrons are attracted to each other -- protons are positively charged while electrons are negatively charged. Although, protons and electrons never fully meet (electrons are always buzzing/hovering around the outside of the nucleus where the protons are).

The configuration of an atom (protons/neutrons/electrons) is what allows us to predicate how one element may react to another element. For example, certain elements may attract, repel, bond, swipe electrons, etc..

The number of protons are what defines the type of atom/element. For example, hydrogen has 1 proton, helium as 2, lithium has 3, etc.. The number of neutrons and electrons can change without changing the type of element as long as the number of protons remain the same.

The periodic table below orders elements/atoms by the number of protons (also called the atomic number)...

When atoms bind together, they form a molecule. Each type of molecule has the same configuration of atoms -- same atoms in the same numbers, structured/shaped similarly. For example, a water molecule is made up of 2 hydrogen atoms and 1 oxygen atom binding together in a house-roof shape...

A monomer is a special designation for atoms/molecules that are able to join with other monomers to create even larger molecules. The process of joining is called polymerization and the resulting molecule is called a polymer.

If the monomers that make up a polymer are all the same, the polymer is called a homopolymer. Otherwise, it's called a heteropolymer / copolymer.

For example, the glucose molecule is a monomer. It can combine with other glucose molecules to create the glycogen molecule, which is a polymer / homopolymer. Other examples of polymers (according to Wikipedia): amino acids and nucleotides (DNA).

Polymers are often referred to as macromolecules -- molecules that have a very large number of atoms.

An ion is a charged atom or molecule. A charged atom/molecule just means that it has an unequal number of protons and electrons:

• if protons > electrons (more protons), it's called a positively charged ion / positive ion.
• if protons < electrons (more electrons), it's called a negatively charged ion / negative ion / ANION.
• if protons == electrons, it's a neutral (no charge).

Ions are always trying to lose their charge and become neutral, either by giving up an electrons or pulling in an electrons such that the the number of protons and electrons become equal. As such, ions will attract towards oppositely charged ions and repel from similarly charged ions:

• negative ions are attracted to positive ions and repelled from negative ions.
• positive ions are attracted to negative ions and repelled from positive ions.

pH

pH stands for potential of hydrogen and it's the measure of positively charged hydrogen ions in a solution. The more...

• the more acidic something is, the more positively charged hydrogen ions it has.
• the more basic (alkaline) something is, the more reactive it is to positively charged hydrogen ions (it wants to give off electrons to those hydrogen ions).

pH is scaled logarithmically from 1 to 14. Each notch on the scale moves the acidity/basicity by a factory of 10. Going...

• back a notch (-1) increases acidity / decreases basicity by a factor of 10.
• forward a notch (+1) decreases acidity / increases basicity by a factory of 10.

For example, going from 7 to 4 increases acidity by 1000x times / decreases basicity by 1000x.

The closer to...

• 1 something is, the more acidic it is (more positively charged hydrogen ions) and the more sour/sharp it tastes.
• 14 something is, the more basic it is (more stuff that can react with positively charged hydrogen ions) and the more bitter it tastes.
• 7 something is, the more neutral it is (not reactive).

Carbohydrate Molecules

Carbohydrates (also called saccharides) are molecules that consist of a mix of carbon, hydrogen, and oxygen atoms. In biological systems, carbohydrates are often associated with...

• being a source of energy
• providing a structural role (for plants / certain plants).

The term monosaccharide is just means a carbohydrate that's a monomer (e.g. glucose). Similarly, the term polysaccharide means a carbohydrate built from other monosaccharides (e.g. glycogen is made of chained glucose).

Protein Molecules

Proteins are molecules that consist of monomers called amino acids. The amino acids get chained together into a polymer called a polypeptide chain, and one or more polypeptide chains fold to a 3D structure and combine to become a protein. The 3D structure / shape of the protein (how its folded) is what gives it its abilities.

In biological systems, proteins are often associated with that facilitating some biological function. For example, the protein protease is responsible for breaking down food.

The basic structure of an amino acid is as follows. The R is a placeholder that, when set, defines what type of amino acid it is...

Lipid Molecules

Lipids are molecules that are somewhat not water soluble -- meaning that they have parts that resist water but maybe also parts that are attracted to water. In biological systems, lipids are often associated with...

• energy storage (fats)
• cellular membranes (phospholipids)

Water Molecule

Water is essential to life -- it has unique properties that almost all biological processes depend on.

Recall that...

1. a water molecule consists of 2 hydrogen atoms connected to an oxygen atom via covalent bonds. A covalent bond is a pair of electrons that both atoms share, thus bonding the atoms together.
2. the position of an electron is based on probability. Electrons aren't fixed in a certain position or neatly orbiting around a nucleus as certain diagrams show. Rather, they're constantly buzzing/hopping around the nucleus. Depending on their environment, they may be more likely to be at certain locations vs other locations.

Oxygen atoms are extremely electronegative, meaning that oxygen has the propensity to pull the buzzing/hopping electrons more around itself than the atoms it's bound to. As such, in a water molecule, the electrons will spend more time solely around the oxygen atom than they do the hydrogen atom or a position that binds the hydrogen and oxygen together. This is what gives the oxygen atom in a water molecule a weakly negative charge (as indicated by δ-) while the hydrogen atoms have a weakly positive charge (as indicated by δ+). These types of charged molecules are called polar molecules.

This weakly negative / weakly positive charge is what gives water several of the unique properties that biological properties depend on. Water molecules have a tendency to gravitate towards each other because the weakly negative oxygen atoms and the weakly positive hydrogen atoms of different water molecules attract. This attraction is called a hydrogen bond. Hydrogen bonds are weaker than covalent bonds in that the bonds aren't really solid -- water molecules can easily break off and go past each other.

The weak attraction between water molecules is also what makes water a solvent. So long as they're polar molecules, other molecules can travel inside of water using the same attraction from weakly negative / weakly positive charges -- they gravitate and float around water molecules just as other water molecules do. For example, the cytoplasm of a cell is a solvent (mostly water). It works because other molecules in the cytoplasm (e.g. cellular machinery) can float around / travel around using the weakly negative / weakly positive charges.

Water is called a universal solvent because it can dissolve more molecules than other other liquid. Note that the term universal doesn't mean that it can dissolve everything, just that it can dissolve more things than the others.

The properties that make water conducive for biological processes to operate:

• Fluid under normal conditions - under normal temperatures, pressures, etc.. there's cohesion between other water molecules (fluid) / adhesion between water molecules and other polar molecules / ions (solvent).
• Universal solvent - Water dissolves more things than any other liquid (more things doesn't mean everything).
• High heat capacity - Because it takes a lot of energy to heat up water, its temperature can remain relatively stable as the environment around it changes (temperature regulation).
• High heat of vaporization - As water evaporates, it traps heat from whatever its on (e.g. human body) and releases it into the environment (temperature regulation / cooling).
• Less dense as a solid - As water freezes it forms crystals that space the molecules away from each other. As such, it becomes less dense than liquid water and ends up floats on top. This means bodies of water can freeze over but life can continue operating in the liquid underneath the frozen ice.

Other terminology related to water:

• Molecules that are charged are called polar molecules (e.g. the water molecule is a polar molecule because of its weakly positive / weakly negative charge).
• Molecules / ions that are charged and mixed with a solvent are called solutes.
• Molecules that are attracted to water are called hydrophilic.
• Molecules that are repelled from water are called hydrophobic.
• Molecules that have parts that are hydrophilic as well as parts that are hydrophobic are called amphipathic

Cells

Cells are the basic unit of living things / the building blocks of life. They're tiny structures that encapsulate information and machinery that allows them to replicate/reproduce and perform other important functions (e.g. appendages to move around).

There are 2 types of cells: eukaryotic and prokaryotic. There main differences between them are that...

1. the guts of eukaryotes are organized into organelles (membrane-bound compartments) where each one is responsible for some functionality, while prokaryotes have no organelles at all (guts are free floating).
2. the DNA in eukaryotes into multiple independent segments (chromosomes), while prokaryotes have a single circular chain.

Other differences between eukaryotes and prokaryotes ...

Features

Different cell species vary in features. The subsections below detail common cell features (not exhaustive).

Some features are only present in certain cell speicies (e.g. only some cells have a flagellum tail) while other features are present in all cells but in different amounts (e.g. every cell has cytosol but larger cells have more cytosol).

Cytoplasm

The cytoplasm (both eukaryotic and prokaryotic) is the insides/guts of a cell. Cytosol refers to just the fluid, while cytoplasm refers to fluid as well as everything else inside the cell.

Every cell has cytoplasm.

Membrane

The plasma membrane (present in both eukaryotic and prokaryotic cells) is the thing encapsulating the cytoplasm. It's what keeps the guys of the cell inside and controls the movement of substances coming into / going out of the cytoplasm.

Every cell has a membrane encapsulating its cytoplasm. Membranes in general follow the fluid mosaic model.

The term membrane can refer to either the plasma membrane or the membrane of a eukaryotic cell's organelle. How you should interpret it depends on the context in which its used.

Facts about cell membranes:

• Membranes have other molecules embedded in them for identification, moving stuff in/out, etc.. (see fluid mosaic model).
• Membranes are semipermeable. Uncharged substances such as carbon dioxide and oxygen move across fine, while charged ions or large molecules require either
  • membrane proteins such as a carrier protein or a channel protein (see fluid mosaic model).
  • membrane wrapper (see golgi).

Cell Wall

The cell wall (present in both eukaryotic and prokaryotic cells) is a stiff layer around the membrane meant for protection. Not all cells have a cell wall -- for example, animal cells don't but plant cells do. Technically, the cell wall (if it exists) isn't considered to be part of the cell. The membrane and everything in it is.

The material states that cell walls...

1. provide an extra layer of protection.
2. help maintain shape.
3. help prevent dehydration.

Almost all prokaryotes have cell walls. Only some eukaryotes have cell walls (e.g. fungi and plants). The material says that cell walls for most bacteria are made up of a molecule called peptidoglycan, but it can be different for other cells. For example, this link says that plant cells have cell walls made up of cellulose.

Capsule

The Capsule (present in prokaryotic cell only) is the outermost layer of some types of cells (typically bacteria cells). Capsules are made up of carbohydrates and there mainly to help the cell stick itself to the environment.

Ribosome

Ribosome (present in both eukaryotic and prokaryotic cells) are tiny molecular machines inside the cytoplasm that take in mRNA molecules (portions of DNA that have been written out) and produce proteins. Ribosomes themselves are structures made of proteins and RNA.

Ribosomes can either be floating around in the cytoplasm (called free ribosome) or be embedded in the membrane of endoplasmic reticulum.

Appendage

Some cells have appendages that help them move (or stay put). There are different types of appendages...

• Flagellum are tails that extend from the cell (e.g. tail on a sperm cell). There can be more than 1 flagellum.
• Cilia are much smaller hair-like appendages used to help move the cell itself or things in the vicinity of the cell.
• Fimbriae are much smaller hair-like appendages used to help attach to host cells and surfaces (e.g. bacteria cells).
• Pili are much smaller hair-like appendages used to help transfer DNA between cells and/or to help move (e.g. bacteria cells).
• Pseudopodia are much larger leg-like appendages used to crawl (e.g. amoeba cells).

Eukaryotic Cells

Eukaryotic cells are typically larger and have membrane-bound sub-compartments, called organelles, that hold in the guts of different regions of the cell. For example, their DNA is encapsulated in a organelle called the nucleus.

Eukaryotes have their DNA broken up into multiple strands. They can either be single-cellular organisms (e.g. amoeba) or multi-cellular organisms (e.g. human). Single-cellular organism that are eukaryotic are called protists.

The following are descriptions for some of the organelles shown in the diagram above.

• Nucleus - See nucleus section.
• Endoplasmic Reticulum - See endoplasmic reticulum section.
• Golgi - See golgi section.
• Mitochondria - See mitochondria section.
• Lysosome (mostly animal) - See lysosome section.
• Peroxisome - See peroxisome section.
• Chloroplast (plant / algae) - See chloroplast section.
• Vacuole (mostly plant / algae) - See vacuole section.

Nucleus

Nucleus is an organelle that contains DNA (genetic information required for the functioning and replication). Both prokaryotic and eukaryotic cells have DNA, but only eukaryotic cells have a nucleus. In prokaryotic cells, the DNA flows around freely instead of being encapsulated in a nucleus.

Most eukaryotic cells contain a single nucleus, but some contain can have 0 and others can have more than one. An example of 0 is blood cells -- mature blood cells don't have any DNA, therefore no nucleus. An example of more than 1 is the organism Oxytricha trifillax -- it contains 2 nuclei, each containing different DNA (its DNA is fragmented across 2 nuclei).

Endoplasmic Reticulum

Endoplasmic Reticulum is layered membrane (organelle?) that surrounds the nucleus and is directly connected to pores on the nucleus. Large portions of the endoplasmic reticulum's membrane have ribosomes attached. The parts that have ribosomes attached are called rough endoplasmic reticulum while the parts that don't are called smooth endoplasmic reticulum.

Recall that ribosomes are what translate mRNA to proteins. Since the endoplasmic reticulum is directly connected to the nucleus (via pores on the nucleus), it provides a fairly straight-forward path for protein generation: mRNA produced in the nucleus...

1. travels to the endoplasmic reticulum via the connected pores,
2. then travels to the membrane of the endoplasmic reticulum where it ends up hitting ribosomes embedded in the (thereby producing proteins).

Golgi

Golgi are layered membrane (organelle?) that look similar to rough endoplasmic reticulum but aren't attached to the nucleus. Golgi package molecules (e.g. proteins) for travel to either another part of the cell or outside of the cell. They do this by pinching off parts of their membrane to wrap around the molecule.

They're also responsible for building lysosomes (cell digestion machines).

Mitochondria

Mitochondria are organelles responsible for cellular respiration: the process of producing Adenosine Triphosphate (ATP) from molecules such as sugars. ATP is a chemical that provides energy to drive various biological processes (e.g. muscle contractions). As such, mitochondria are often referred to as "the power house of the cell."

The major parts of chloroplast are...

• mitochondrial envelope - 2 membrane layers that have a gap between them. Holds the guts in.
• matrix - Internal fluid of mitochondria. Contains the guts (ribosomes, mitochondrial DNA, and more).
• cristae - Long caverns that encapsulate and connect different parts of the matrix.

Mitochondria have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis).

Unlike how normal offspring DNA gets produced by mixing DNA from both parents, mitochondrial DNA comes entirely from the mother's side.

Lysosome

Lysosomes are organelles (animal cells only) that help break down waste products / foreign substances by containing various enzymes and maintaining an acidic pH. Lysosomes are more often found in animals cells than plant and algae cells.

Peroxisome

Peroxisomes are organelles that are similar to Lysosomes -- both are small organelles that break down unwanted substances. The difference is that peroxisomes have different types of enzymes that require oxygen (oxidative enzymes).

Chloroplast

Chloroplasts are organelle (only plant and algae cells) responsible for photosynthesis. Photosynthesis is the process of taking in light and using it to build sugars from water and carbon dioxide. Those sugars are then used by the mitochondria to produce energy in a process called cellular respiration.

The major parts of chloroplast are...

• chloroplast envelope - 2 membrane layers that have a gap between them. Holds the guts in.
• stroma - Internal fluid of chloroplast (chloroplast's version of cytosol).
• thylakoid - Membrane-bound discs. The membrane contains light-harvesting substances while the space inside (also called lumen) is hollow.
• grana - Stack of thylakoids. These stacks are interconnected. The singular of grana is granum.

Chlorophyll is a pigment / compound found in chloroplast that absorbs light and uses it to produce carbohydrates. It's found in the thylakoid membrane as well as the stroma, and it only absorbs red and blue light (while reflecting green).

Like mitochondria, chloroplast have their own independent DNA (different from the DNA in the nucleus). It's speculated that at some point in the past they may have been independent single-cell organisms that formed a symbiotic relationship with a larger cell by living in it, eventually becoming part of the cell (endosymbiosis). A descendant of that organism may be cyanobacterium, which has a similar ability to generate sugars from light (see Wikipedia).

Vacuole

Vacuoles are organelle (mostly plant and algae cells) responsible for storage (water, food, waste?) and enzymes that help break things down. Vacuoles are typically found in plant and algae cells, but may also exist in animal cells. The ones in plants / algae tend to be much larger.

Vacuoles are often responsible for a plant's shape. For example, a well watered plant will be upright and spry because its vacuoles are full. A plant that isn't as well watered may be sagging down or wilting because the vacuoles are less full

Prokaryotic Cells

Prokaryotic cells: These cells are typically smaller and don't have organelles. For example, their DNA is free-floating in the cell (it's free floating but stays mostly in the center area called the nucleoid).

Prokaryotes have a single circular-strand of DNA. They can only be single-cellular organisms (e.g. bacteria).

Fluid Mosaic Model

The fluid mosaic model is the accepted model for how cell membranes work. The model says that a cell membrane is composed of a phospholipid bilayer with proteins, lipids, and carbohydrates floating around on either side or embedded in between.

A phospholipid is a amphipathic lipid molecule that involves a phosphate group. The...

• bulbus phosphate group at the top is hydrophilic -- it has a charge and as such is attracted to water (either the cytoplasm or the fluid outside the cell).
• long fatty acid tails are hydrophobic -- they have no obvious charge and as such aren't attracted to water.

As such, phospholipids have a natural tendency to form as a phospholipid bilayer (2 layers attached together, called a liposome) or a ball (called a micelle). The hydrophilic heads are going to point towards the water causing the hydrophobic tails to point at each other.

How fluid a phospholipid bilayer is depends on the types of phospholipid molecules that make it up and the temperature. Phospholipid molecules have 2 fatty acid tails. The fatty acid tails can be either...

• both saturated (straight tails)
• one saturated (straight tail) and one unsaturated (bent tail).

At cooler temperatures, phospholipids that have 2 saturated fatty acid tails (straight tails) tend to get more rigid / dense because they can more easily pack together. Phospholipids with unsaturated fatty acid tails (bent tails) don't end up getting as rigid / dense, allowing the membrane to stay fluid at lower temperatures. Cholesterol embedded in the phospholipid bilayer also helps it stay more fluid at lower temperatures.

Examples of molecules that can be embedded in or attached to the phospholipid bilayer include...

• Glycolipids / Glycoproteins - These are lipids and proteins with carbohydrates attached to them and are typically found pointing outside of the cell. These carbohydrates are how a cell identifies if a neighbouring cell is foreign or not.
• Integral proteins - Proteins that are partially hydrophobic. Either one end of the protein is anchored inside the membrane or the protein is fully going through the membrane.
  • Transmembrane proteins - Proteins that have one end inside the cytoplasm and the other outside of the cell. Typical use case for these types of proteins is moving substances from inside the cell (cytoplasm) to outside the cell and vice-versa: channel proteins and carrier proteins.
• Peripheral proteins - Proteins that are found on the surface of the protein (either on the cytoplasm side or the outside side). Unlike integral proteins, they don't have any portion going inside the membrane. As such, they more freely move around compared to integral proteins.
• Cholesterol - Sits inside of the membrane to help ensure that the membrane doesn't become too stiff.

The term facilitated diffusion refers to the movement of molecules across the membrane via proteins embedded in the membrane (e.g. channel proteins and/or carrier proteins). These molecules wouldn't be able to cross the membrane by themselves. For example, the sodium potassium pump (carrier protein) helps sodium and potassium ions move across the cell membrane by opening/closing its gates.

History of Modern Cell Theory

The first record of a cell was in 1665 when Robert Hooke published a book called The Micrographia. The book contains drawings of observations he made while looking at various dead organisms through a rudimentary microscope.

A few years later, a Dutch lenscrafter by the name of Antonie Van Leeuwenhoek decided to use his expertise to craft a better microscope to better observe living cells / organisms. For example, he was able to observe sperm and Protists (unicellular organisms while he dubbed animalcules).

In the 1830s, Matthias Schleiden and Theodore Schwann began laying the groundwork for modern cell theory. They came up with the idea that...

1. all life is composed of one or more cells.
2. a cell is the basic unit of life.

They also suspected that cells come from other cells, but didn't know for sure if that was the only way they were produced. It was Robert Remak that in the mid-1800s established that...

3. all cells come from other cells.

It's still an open question as to how the first / initial cell came to be. The current working theory is that, 3.5 billion years ago, phospholipids (the molecules that form the membrane of a cell) naturally form bilayers and connect in a circle. A membrane may have naturally encapsulated a set of arbitrary self-replication molecules (e.g. protein or RNA) and that's how the first cell began growing and splitting off.

Enzymes

An enzyme is a molecule that takes in a specific set of input molecules and transforms them into a specific set of output molecules. The transformation takes the inputs and either ...

• assembles them into new larger molecules (N to 1).
• separates them into smaller molecules (1 to N).
• transfers fragments between them (N to N).

Enzymes facilitate these transformations by lowering the activation energy ($E_A$) required for the chemical reactions to take place. Normally this excess energy would come in the form of heat, but enzymes use different mechanisms such as...

• temporarily contorting input molecules
• temporarily pulling away some charge from adjacent atoms of input molecules

... such that other atoms can get close enough to bond.

An enzyme is almost always a protein molecule but can also be a RNA-like molecule called a ribozyme.

The general terminology for enzymes are as follows:

• Substrate / Reactants refers to the input molecules of an enzyme.
• Product refers to the output molecules of an enzyme.
• Metabolite refers to either a substrate or product.
• Metabolism is the total sum of all the chemical reactions that take place inside of a cell. These reactions happen via enzymes.
• Active sites are the physical locations that substrates float into on an enzyme.
• Catalysis / Catalyze is the term for increasing the rate / probability of a chemical reaction. Enzymes perform catalysis.
• Catalysts are entities that speed up chemical reactions but don't change in the process (reaction happens but catalyst remains). Enzymes are catalysts.

Enzymes have a limited set of substrate types that they accept. A substrate will bind to the active site of the enzyme only if it fits into the active site. For example, the following diagram shows 2 substrates binding to an enzyme, the enzyme facilitating their their assembly, then releasing back out.

It was previously thought that enzymes had a “lock-and-key” model, similar to how puzzle pieces fit together. Later on it was found out that an enzymes actually induce fit by changing shape slightly when they bind with substrates, such that they can better hold on to those substrates.

Examples of enzymes and what they do:

• protease → breaks up protein molecules to smaller protein molecules.
• sucrase → breaks up sucrose molecules to simpler sugar molecules.
• RNA polymerase → scans over DNA... splitting it, generating mRNA, and stitching it back up.

Metabolic Pathway

A metabolic pathway is a network/graph of enzymes that produces a final resulting molecule. Each enzyme produces molecules that feed into other enzymes in the pathway, eventually forming the final molecule. The term intermediate refers to an output of one enzyme that’s used as an input by another.

For example, the following graph is the metabolic pathway for gamma-hydroxybutyric acid...

Anabolism

Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).

The process that builds up a molecule from smaller molecules is called anabolism. An enzyme takes in the molecules and creates bonds between them via an endergonic reactions: energy is stored as bonds between the smaller molecules thereby forming the larger molecule.

An example of anabolism is photosynthesis: plants will bond carbon dioxide gas ($CO_2$) with water ($H_2O$) using energy from the sun, creating sugar ($C_6H_{12}O_6$)

$6CO_2 + 6H_2O + energy \to C_6H_{12}O_6 + 6O_2$

Catabolism

Metabolism can be broken down into 2 categories: anabolism (building-up) and catabolism (breaking-down).

The process that breaks down a large molecule into smaller molecules is called catabolism. An enzyme takes in a larger molecule breaks up some of its bonds via exergonic reactions: energy used as bonds in the molecule are release thereby breaking it up into smaller molecules.

An example of catabolism is cellular respiration: cells will break down the bonds in glucose ($C_6H_{12}O_6 + 6O_2$) to release energy, splitting into carbon dioxide ($CO_2$) and water ($H_2O$)

$C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O + energy$

Nucleotides

Nucleic Acid is a molecule (heteropolymer) that's built up from other molecules called nucleotides (monomers). Nucleic acid comes in 2 flavours: DNA and RNA. Each nucleotide consists of a sugar molecule (ribose in RNA / deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base.

There are 5 base.:

• A (adenine)
• C (cytosine)
• G (guanine)
• T (thymine) / U (uracil)

Two nucleotides connected together are called a base pair. The rules to base pairs are:

• A only ever binds to T/U (e.g. AT or TA in DNA, AU or UA in RNA)
• G only ever binds to C (e.g. GC or CG)

DNA

Deoxyribonucleic acid (DNA) is a nucleic acid molecule that contains the instructions needed for the growth/functioning/maintenance of an organism. Depending on the type of organism, DNA is located in different parts fo the cell.

• For prokaryotes, DNA is free-floating in the cytoplasm.
• For eukaryotes, DNA is isolated in the nucleus (nuclear DNA). Their mitochondria and chloroplast also have their own DNA.

DNA is composed of two strands of nucleotides that connect at various points in between. The order these nucleotides appear in defines the genetic information/instructions of the organism. For example, a string/sequence of DNA bases: ATATTTTCGATATCCACCA.

DNA strands can be made up of 4 different nucleotide types (bases):

• A (adenine)
• C (cytosine)
• G (guanine)
• T (thymine)

The two nucleotides that make up a connection are called a base pair. In DNA, the rules to base pairs are...

• A only ever binds to T (e.g. AT or TA)
• G only ever binds to C (e.g. GC or CG)

Terminology specific to DNA:

• genome - The entire set of DNA for an organism. For eukaryotes, this refers to nuclear DNA, not the independent DNA carried by organelles such as mitochondria.
• gene - A section of an organism's DNA that contains instructions for some functionality, typically for building some protein.

RNA

Ribonucleic acid (RNA) is a nucleic acid molecule used in various ways to facilitate building proteins. It can also act as an enzyme (ribozyme) or contain the genetic information for some viruses.

RNA is commonly composed of a single strand that folds over onto itself.

RNA strands can be made up of 4 different nucleotide types (bases):

• A (adenine)
• C (cytosine)
• G (guanine)
• U (uracil)

The two nucleotides that make up a connection are called a base pair. In RNA, the rules to base pairs are...

• A only ever binds to U (e.g. AU or UA)
• G only ever binds to C (e.g. GC or CG)

Unlike DNA, RNA is transient (lasts for minutes) and comes in multiple flavours:

• mRNA or messenger RNA - Carries information from DNA to the ribosomes detailing a protein to build. Ribosomes are the parts of cells that synthesize proteins.
• tRNA or transfer RNA - Brings to the ribosome the amino acids required to build the protein that the mRNA is requesting.
• rRNA or ribosomal RNA - Makes up a large portion of the ribosome (60%). The rest of the ribosome is protein.

Chromosome

The genome of eukaryotes are split into linear strands of DNA. These linear DNA strands come in 3 forms...

1. Chromatin is the normal state, where the DNA is loosely floating around with structural proteins called histones.
2. Chromatid is the packed form of chromatin, where the DNA is packed using even more structural proteins called scaffold proteins while being replicated. The original chromatid instance and the new chromatid instance are attached together, and they're referred to as sister chromatids.
3. Chromosome is essentially the same thing as sister chromatids: the original chromatid instance and the new chromatid instance attached together.

At a high-level, the process of DNA replication can be boiled down to 3 steps...

1. The chromatin is copied. Each instance is now referred to as a chromatid and is attached to the other (sister chromatid) via proteins called cohesins.
2. The sister chromatids condense and start to separate in an X shape. The section they remain connected at is a segment of DNA called the centromere.
3. The sister chromatids are pulled apart. Each instance is now reverted back to being referred to as chromatin.

Most eukaryotic species are diploid, meaning that their linear DNA strands come in matching pairs where each pair contains different versions of the same set of genes (homologous pairs). When these organisms reproduce, they generate special cells known as haploid cells that only contain 1 strand from each pair. Two haploid cells mix their DNA to create a final diploid offspring (e.g. a sperm cell and an ova cell).

Certain diploid eukaryotic species (some mammals/snakes/insects/etc..) have an extra pair that aren't alternate versions of each other but instead are totally different and used to determine the sex of the offspring. This extra pair are called sex chromosomes / XY chromosomes, and it determines the sex of the organism. The X and the Y refer to the chromosome types that can appear in the pair -- XX results in a female, while XY results in a male.

The non-sex chromosome pairs are referred to as autosomes.

Reproduction

Reproduction is when an organism generates offspring. It comes in 2 forms: asexual and sexual.

Asexual reproduction is when offspring is created using the genetic material from 1 parent. The offspring are essentially copies of the parent in terms of their genetic material (clone). Examples of asexual reproduction include:

• Binary fission - Process of cloning a prokaryotic cell and certain organelle inside of eukaryotic cell (e.g. mitochondria).
• Mitosis - Process of cloning a eukaryotic cell.
• Budding - When a growth on a plant or animal breaks off, that broken piece is the offspring.
• Fragmentation - When an organism breaks into two or more pieces, each fragment grows back into a whole.
• Parthenogenesis - When an animal lays an egg but that egg already has all the genetic information needed to develop (it doesn't need to be fertilized).

Sexual reproduction is when offspring is created by fusing genetic material from 2 parents. The offspring has a mixture of genetic material from both parents. An example of sexual reproduction is when a gamete cells merge to create the offspring. Gamete cells have half the genetic information from the original parent, and when they merge they mix that genetic material to create the new genetic material for the offspring. Male gamete cells are called sperm, while female gamete cells are called ova or eggs.

Adenosine Triphosphate

Adenosine Triphosphate (ATP) is a molecule that provides energy to drive various biological processes (e.g. muscle contractions). The third phosphoral group at the very end has a high-energy bond. When broken, energy is released and the resulting molecules are the broken up phosphoral group and Adenosine Diphosphate (ADP).

ATP is produced in the mitochondria. Similar to how the mitochondria is referred to as the powerhouse of the cell, ATP is often referred to as the energy currency of the cell / energy store for the cell.

Transport

There are 2 different types of mechanism used to transport molecules in and out of a cell: passive transport and active transport.

Passive transport is when molecules naturally move towards the gradient. In this context, gradient refers to the natural direction in which things are supposed to go -- no explicit energy is needed to move/push it along, it just moves in that direction by virtue of some implicit property.

• A concentration gradient is when the concentration of a molecule evens out in a volume just by virtue of the molecules randomly bouncing around (diffusion). For example, gas pumped into a vacuum will end up filling the vacuum evenly (more-or-less) -- traveling from areas of high concentration to areas of low concentration.

  

  NOTE: All this is saying is that if you have a group of items clustered in a single area, each traveling at a different speed / direction, will spread out over time.

• An electrical gradient is when molecules flow in some direction because their electrical charges attract. For example, a negatively charged molecule will gravitate towards a positively charged molecule. Similarly, a negative molecule will gravitate away from from other negative molecules / a positive molecule will gravitate away from other positive molecules.

  

• An electrochemical gradient is a combination of both a concentration gradient and an electrical gradient.

Active transport is when molecules use energy (e.g. ATP) to move against their gradient. It's the opposite of passive transport -- energy is explicitly used to drive a molecule to where it naturally / normally wouldn't go. An example of active transport is the "sodium potassium pump" enzyme: ATP is used to force open/close the ends of the enzyme, which allow sodium and potassium to be exchanged across the cell membrane.

Note that the active transport in the example above is the opening/closing of the enzyme ends, not the exchange of sodium and potassium. Energy (ATP) is being used to shape-shift the enzyme to open/close (active transport) while the sodium and potassium are passively entering and exiting the gates (passive transport via facilitated diffusion).

Osmosis

Osmosis is the passive transport of solvent molecules (typically water), across a semipermeable membrane, from areas where solutes are less concentrated to areas where solutes are more concentrated.

For example, imagine you have a semipermeabl membrane that allows water molecules (solvent) to pass but not sodium (solute). That membrane is separating 2 regions, where the ...

• left region is a solution of 25% sodium (solute) and 75% water (solvent).
• right region is a solution of 75% sodium (solute) and 25% water (solvent).

There will be a net movement of some water molecules from the left region (lower solute concentration) to the right region (higher solute concentration).

There are 2 reasons why osmosis happens. The first is that the semipermeable membrane will only allow certain types of molecules to pass through. If the semipermeable membrane is gated by ...

• size, the solute molecules may be too large to pass through.
• charge, the solute molecules may not have the required charge to pass through.

The higher the concentration of solute molecules, the less likely it is for the solvent molecules to reach a pore in the semipermeable membrane. The side with the lower concentration of solute molecules is more likely to have a solvent molecule reach a pore than the other way around.

The second reason is that, depending on the charge of solvent and charge of solute, the solvent may be attracted to the solute. More solute = more chance that a solvent gets attracted to it instead of crossing a pore in the membrane. For example, if the solvent is water and the solute is sodium, the weakly negative charge of the oxygen atom in a water molecule may get attracted to the positive charge of the sodium ion.

Tonicity is the amount of pressure applied to a semipermeable membrane due to osmosis. In other words, it's the amount of water that flows in or out of a cell due to the type of solution it's put in. A ...

• hypertonic solution is one that has more solutes than the cell, meaning the inside of the cell loses water (cell shrivels).
• hypotonic solution is one that has less solutes than the cell, meaning the inside of the cell gains water (cell swells).
• isotonic solution is one that has a roughly equal amount of solutes, meaning the cell's water content remains the same.

The following is a micrograph of the red blood cells in solutions of different tonicity. Notice how they shrivel in a hypertonic solution (lose water) and expand in a hypotonic solution (gain water).

Photosynthesis

Photosynthesis is the process by which certain organisms convert light energy (photons) to chemical energy (sugars). These organisms are called Photoautotrophs, and they include ...

• plants and algae (eukaryotic), which perform photosynthesis via their chloroplast.
• cyanobacterium, which are bacteria that can generate their own food.

The overall chemical reaction for this is $6CO_2 + 6H_2O + energy \to C_6H_{12}O_6 + 6O_2$. Carbon dioxide gas ($CO_2$) bonds with water ($H_2O$) using energy from the sun (photons), creating glucose ($C_6H_{12}O_6$).

This reaction happens in 2 steps:

1. Light-dependent reactions: Energy molecules are created from water and photos, with oxygen being a byproduct.

   This occurs in a thylakoid membrane.

   

2. Calvin cycle: It's a cyclical process that requires multiple iterations (3?) to produce a single glucose molecule. Each cycle, ATP and NADPH are used for energy (producing ADP and NADP+ respectively), while the carbon dioxide ($CO_2$) is used as a source of carbons for the resulting glucose.

   This occurs in the stroma.

   

The following workflow diagram provides a ultra-simple high-level overview of the processes that take place. Note that this doesn't specify how many of each molecule get input / output, nor does it provide a complete set of a input / output molecules for each reaction.

Cellular Respiration

Cellular respiration is the process by which certain organisms convert glucose (sugar) to energy. These organisms include ...

• eukaryotic cells, which perform cellular respiration via their mitochondria.
• bacteria which share their ancestry with mitochondria.

The overall chemical reaction for this is $C_6H_{12}O_6 + 6O_2 \to 6CO_2 + 6H_2O + energy$. Glucose ($C_6H_{12}O_6$) and oxygen ($O_2$) break down into carbon dioxide gas ($CO_2$), water ($H_2O$), and energy (roughly 38 ATP molecules and some heat).

The reaction happens in 3 steps:

1. Glycolysis: The carbon backbone of the glucose molecule is split, creating 2 Pyruvate molecules along with water and several other molecules. This is an anaerobic process (no oxygen needed) that nets 2 ATP. This happens in the cytoplasm of cells.

   

2. Krebs cycle: The pyruvate molecules get further sliced and diced with other molecules. This is an aerobic process (requires oxygen) that nets 2 ATP. This happens in the matrix of the mitochondria.

   

3. Oxidative phosphorylation: Produces around 34 ATP. This is an aerobic process (requires oxygen) that nets roughly 34 ATP (bulk of conversions). This happens in the electron transport chain section of the mitochondria (inner membrane).

   

Because the Krebs cycle and the oxidative phosphorylation are aerobic processes (require oxygen), if no oxygen is present the output of glycolysis goes through a process called fermentation. Fermentation is an anaerobic process (no oxygen required). Depending on the organism, it'll end up producing either...

• alcohol via alcohol fermentation (e.g. yeast).
• lactic acid via lactic acid fermentation (e.g. humans and mammals).

Fermentation does produce ATP, but much less so than Kerbs cycle + oxidative phosphorylation.

For example, if a human is vigorously running, that human may not have enough oxygen available to trigger the Krebs cycle / oxidative phosphorylation (steps 2 and 3). As such, the output from glycolysis (step 1) will end up going through lactic acid fermentation instead.

The following workflow diagram provides a ultra-simple high-level overview of the processes that take place. Note that this doesn't specify how many of each molecule get input / output, nor does it provide a complete set of a input / output molecules for each reaction.

Sodium Potassium Pump

The sodium potassium pump is an transmembrane enzyme that allows the exchange of sodium ions and potassium ions across the cell membrane by opening and closing its ends.

Only 1 end of the enzyme is open at a time. When the...

• intracellular end is open, the enzyme has an affinity for 3 sodium ions followed by an affinity for ATP.
• extracellular end is open, the enzyme has an affinity for 2 potassium ions.

Since both potassium and sodium have a positive charge and an an unequal number are being exchanged each cycle (3 sodium out vs 2 potassium in), the intracellular space will be more positive than the extracellular space.

This charge difference is further reinforced by membrane channel proteins which allow potassium ions to flow across the membrane (potassium channels). Since there's a higher concentration of potassium ions inside the cell, those potassium ions have a higher chance of flowing through the channel to the outside. Some percentage may be impeded by the slightly more positive charge on the outside, but overall more will make it to the outside than stay on the inside.

This charge difference is referred to as the resting membrane potential for a cell.

Microscopy

Microscopes are devices used to magnify (zoom in) on objects, such that you can see things that you normally would be too small to see on your own. The term microscope comes from the words...

• micro, meaning small.
• scope, meaning to look at.

A picture taken through a microscope is called a micrograph. The distinguishing factors for most microscopes or the amount of magnification and the resolution of the output image.

There are different types of microscopes:

• Simple microscopes have just one lense (e.g. magnifying glass).
• Compound microscopes have 2 ore more lenses (e.g. traditional microscopes used in labs).
  • Light microscopes / Brightfield microscopes work by shining a light through the specimen (which can be alive) and into the lens system that eventually reaches your eye. They're the type of microscopes typically used in student labs.
    • Fluorescence microscopes are microscopes that require the specimen being viewed is treated in some way to make it glow, allowing you to highlight parts of the specimen.
    • Confocal microscopes are a special form of fluorescence microscopes that uses a laser to excite a sample and get it to glow fluorescent.
• Electron microscopes use beams of electrons rather than beams of light. They produce very magnified very high resolutions images. But, unlike light microscopes, the specimens being observed are dead because electron microscopes operate in a vacuum.
  • scanning electron microscopes (SEM) work by scanning a beam of electrons over the surface of the specimen to produce an image of the 3D surface.
  • transmission electron microscopes (TEM) work by slicing up the specimen into ultra thin slices and and passing an electron bean through those slices to produce an image of the insides.

Other Terminology

Terminology that's relevant but doesn't fit in any other section goes here.

Density - The mass per unit volume of a substance.

Specific heat capacity - The amount of heat needed to raise the temperature of one gram of a substance by one degree Celsius.

Heat of vaporization - The amount of energy needed to change one gram of a liquid substance to a gas at constant temperature.

Endosymbiosis - A form of symbiosis where one organism lives inside of of the other (e.g. gut bacteria lives in our colon). The prefix endo means within.

Diffusion - A physical process where molecules of a material move from an area of high concentration (where there are many molecules) to an area of low concentration (where there are fewer molecules) until it has reached equilibrium (molecules evenly spread). See more.

Equilibrium - A state in which opposing forces / influences are balanced. In the context of a concentration gradient, it means the state at which a substance is equally distributed throughout the volume that it's in (roughly).

Permeability - The state or quality of a material or membrane that causes it to allow liquids/gases to pass through it.

Semipermeable - The state or quality of a material or membrane that causes it to allow certain types of molecules to pass through it.

Intracellular - The fluid inside of the cell, which is technically on the inside of the cell membrane (cytoplasm).

Extracellular - The fluid outside of the cell.

Aerobic - A biological process that requires oxygen.

Anaerobic - A biological process that doesn't require oxygen.

Fission - The act of dividing or splitting something into two or more parts.

Homologous - Having the same relation, relative position, or structure. Particularly in biology, it s the existence of a shared ancestry between a pair of structures or genes.

Karyotype - Micrograph image of diploid set of chromosomes, grouped in pairs.